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North HL, Fu Z, Metz R, Stull MA, Johnson CD, Shirley X, Crumley K, Reisig D, Kerns DL, Gilligan T, Walsh T, Jiggins CD, Sword GA. Rapid Adaptation and Interspecific Introgression in the North American Crop Pest Helicoverpa zea. Mol Biol Evol 2024; 41:msae129. [PMID: 38941083 PMCID: PMC11259193 DOI: 10.1093/molbev/msae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
Insect crop pests threaten global food security. This threat is amplified through the spread of nonnative species and through adaptation of native pests to control measures. Adaptations such as pesticide resistance can result from selection on variation within a population, or through gene flow from another population. We investigate these processes in an economically important noctuid crop pest, Helicoverpa zea, which has evolved resistance to a wide range of pesticides. Its sister species Helicoverpa armigera, first detected as an invasive species in Brazil in 2013, introduced the pyrethroid-resistance gene CYP337B3 to South American H. zea via adaptive introgression. To understand whether this could contribute to pesticide resistance in North America, we sequenced 237 H. zea genomes across 10 sample sites. We report H. armigera introgression into the North American H. zea population. Two individuals sampled in Texas in 2019 carry H. armigera haplotypes in a 4 Mbp region containing CYP337B3. Next, we identify signatures of selection in the panmictic population of nonadmixed H. zea, identifying a selective sweep at a second cytochrome P450 gene: CYP333B3. We estimate that its derived allele conferred a ∼5% fitness advantage and show that this estimate explains independently observed rare nonsynonymous CYP333B3 mutations approaching fixation over a ∼20-year period. We also detect putative signatures of selection at a kinesin gene associated with Bt resistance. Overall, we document two mechanisms of rapid adaptation: the introduction of fitness-enhancing alleles through interspecific introgression, and selection on intraspecific variation.
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Affiliation(s)
- Henry L North
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Zhen Fu
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Richard Metz
- AgriLife Genomics and Bioinformatics Service, Texas A&M University, College Station, TX 77843, USA
| | - Matt A Stull
- AgriLife Genomics and Bioinformatics Service, Texas A&M University, College Station, TX 77843, USA
| | - Charles D Johnson
- AgriLife Genomics and Bioinformatics Service, Texas A&M University, College Station, TX 77843, USA
| | - Xanthe Shirley
- Animal and Plant Health Inspection Service, United States Department of Agriculture, College Station, TX, USA
| | - Kate Crumley
- Agrilife Extension, Texas A&M University, Wharton, TX, USA
| | - Dominic Reisig
- Department of Entomology and Plant Pathology, North Carolina State University, Plymouth, NC, 27962, USA
| | - David L Kerns
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Todd Gilligan
- Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, CO, USA
| | - Tom Walsh
- Black Mountain Laboratories, Commonwealth Scientific and Industrial Research Organization, Canberra, Australia
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Gregory A Sword
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
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Stahlke AR, Chang J, Tembrock LR, Sim SB, Chudalayandi S, Geib SM, Scheffler BE, Perera OP, Gilligan TM, Childers AK, Hackett KJ, Coates BS. A Chromosome-Scale Genome Assembly of a Helicoverpa zea Strain Resistant to Bacillus thuringiensis Cry1Ac Insecticidal Protein. Genome Biol Evol 2023; 15:evac131. [PMID: 35959935 PMCID: PMC9990077 DOI: 10.1093/gbe/evac131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 11/14/2022] Open
Abstract
Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt-resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.
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Affiliation(s)
- Amanda R Stahlke
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, 10300 Baltimore Avenue, Beltsville, Maryland 20705
| | - Jennifer Chang
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, Mississippi 38776
- USDOE, Oak Ridge Institute for Science and Education, P.O. Box 117, Oak Ridge, Tennessee 37831
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, Iowa 50010
| | - Luke R Tembrock
- USDA, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Identification Technology Program, 2301 Research Boulevard, Fort Collins, Colorado 80526
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Sheina B Sim
- USDA, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Crop and Commodity Protection Research Unit, 64 Nowelo Street, Hilo, Hawaii 96720
| | - Sivanandan Chudalayandi
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, Iowa 50010
| | - Scott M Geib
- USDA, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Crop and Commodity Protection Research Unit, 64 Nowelo Street, Hilo, Hawaii 96720
| | - Brian E Scheffler
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, Mississippi 38776
| | - Omaththage P Perera
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Southern Insect Management Research Unit, 141 Experiment Station Road, Stoneville, Mississippi 38776
| | - Todd M Gilligan
- USDA, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Identification Technology Program, 2301 Research Boulevard, Fort Collins, Colorado 80526
| | - Anna K Childers
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, 10300 Baltimore Avenue, Beltsville, Maryland 20705
| | - Kevin J Hackett
- USDA, Agricultural Research Service, Office of National Programs, Crop Production and Protection, 5601 Sunnyside Avenue, Beltsville, Maryland 20705
| | - Brad S Coates
- USDA, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 819 Wallace Road, Ames, Iowa 50011
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Ke F, Li J, Vasseur L, You M, You S. Temporal sampling and network analysis reveal rapid population turnover and dynamic migration pattern in overwintering regions of a cosmopolitan pest. Front Genet 2022; 13:986724. [PMID: 36110208 PMCID: PMC9469019 DOI: 10.3389/fgene.2022.986724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic makeup of insect pest is informative for source-sink dynamics, spreading of insecticide resistant genes, and effective management. However, collecting samples from field populations without considering temporal resolution and calculating parameters related to historical gene flow may not capture contemporary genetic pattern and metapopulation dynamics of highly dispersive pests. Plutella xylostella (L.), the most widely distributed Lepidopteran pest that developed resistance to almost all current insecticides, migrates heterogeneously across space and time. To investigate its real-time genetic pattern and dynamics, we executed four samplings over two consecutive years across Southern China and Southeast Asia, and constructed population network based on contemporary gene flow. Across 48 populations, genetic structure analysis identified two differentiated insect swarms, of which the one with higher genetic variation was replaced by the other over time. We further inferred gene flow by estimation of kinship relationship and constructed migration network in each sampling time. Interestingly, we found mean migration distance at around 1,000 km. Such distance might have contributed to the formation of step-stone migration and migration circuit over large geographical scale. Probing network clustering across sampling times, we found a dynamic P. xylostella metapopulation with more active migration in spring than in winter, and identified a consistent pattern that some regions are sources (e.g., Yunnan in China, Myanmar and Vietnam) while several others are sinks (e.g., Guangdong and Fujian in China) over 2 years. Rapid turnover of insect swarms and highly dynamic metapopulation highlight the importance of temporal sampling and network analysis in investigation of source-sink relationships and thus effective pest management of P. xylostella, and other highly dispersive insect pests.
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Affiliation(s)
- Fushi Ke
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Jianyu Li
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Liette Vasseur
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Department of Biological Sciences, Brock University, St. Catharines, ON, Canada
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Minsheng You, ; Shijun You,
| | - Shijun You
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- BGI-Sanya, Sanya, China
- *Correspondence: Minsheng You, ; Shijun You,
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Dorman SJ, Hopperstad KA, Reich BJ, Majumder S, Kennedy G, Reisig DD, Greene JK, Reay-Jones FP, Collins G, Bacheler JS, Huseth AS. Landscape-level variation in Bt crops predict Helicoverpa zea (Lepidoptera: Noctuidae) resistance in cotton agroecosystems. PEST MANAGEMENT SCIENCE 2021; 77:5454-5462. [PMID: 34333843 DOI: 10.1002/ps.6585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/25/2021] [Accepted: 08/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Helicoverpa zea (Boddie) damage to Bt cotton and maize has increased as a result of widespread Bt resistance across the USA Cotton Belt. Our objective was to link Bt crop production patterns to cotton damage through a series of spatial and temporal surveys of commercial fields to understand how Bt crop production relates to greater than expected H. zea damage to Bt cotton. To do this, we assembled longitudinal cotton damage data that spanned the Bt adoption period, collected cotton damage data since Bt resistance has been detected, and estimated local population susceptibility using replicated on-farm studies that included all Bt pyramids marketed in cotton. RESULTS Significant year effects of H. zea damage frequency in commercial cotton were observed throughout the Bt adoption period, with a recent damage increase after 2012. Landscape-level Bt crop production intensity over time was positively associated with the risk of H. zea damage in two- and three-toxin pyramided Bt cotton. Helicoverpa zea damage also varied across Bt toxin types in spatially replicated on-farm studies. CONCLUSIONS Landscape-level predictors of H. zea damage in Bt cotton can be used to identify heightened Bt resistance risk areas and serves as a model to understand factors that drive pest resistance evolution to Bt toxins in the southeastern United States. These results provide a framework for more effective insect resistance management strategies to be used in combination with conventional pest management practices that improve Bt trait durability while minimizing the environmental footprint of row crop agriculture. © 2021 Society of Chemical Industry. This article has been contributed to by US Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Seth J Dorman
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- USDA-ARS Forage Seed and Cereal Research Unit, Corvallis, OR, USA
| | - Kristen A Hopperstad
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Brian J Reich
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Suman Majumder
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - George Kennedy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Dominic D Reisig
- Department of Entomology and Plant Pathology, North Carolina State University, Vernon James Research and Extension Center, Plymouth, NC, USA
| | - Jeremy K Greene
- Department of Plant and Environmental Sciences, Clemson University, Edisto Research and Education Center, Blackville, SC, USA
| | - Francis Pf Reay-Jones
- Department of Plant and Environmental Sciences, Clemson University, Pee Dee Research and Education Center, Florence, SC, USA
| | - Guy Collins
- Department of Crop and Soil Science, North Carolina State University, Raleigh, NC, USA
| | - Jack S Bacheler
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Anders S Huseth
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
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Dively GP, Kuhar TP, Taylor S, Doughty HB, Holmstrom K, Gilrein D, Nault BA, Ingerson-Mahar J, Whalen J, Reisig D, Frank DL, Fleischer SJ, Owens D, Welty C, Reay-Jones FPF, Porter P, Smith JL, Saguez J, Murray S, Wallingford A, Byker H, Jensen B, Burkness E, Hutchison WD, Hamby KA. Sweet Corn Sentinel Monitoring for Lepidopteran Field-Evolved Resistance to Bt Toxins. JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:307-319. [PMID: 33274391 DOI: 10.1093/jee/toaa264] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Indexed: 06/12/2023]
Abstract
As part of an insect resistance management plan to preserve Bt transgenic technology, annual monitoring of target pests is mandated to detect susceptibility changes to Bt toxins. Currently Helicoverpa zea (Boddie) monitoring involves investigating unexpected injury in Bt crop fields and collecting larvae from non-Bt host plants for laboratory diet bioassays to determine mortality responses to diagnostic concentrations of Bt toxins. To date, this monitoring approach has not detected any significant change from the known range of baseline susceptibility to Bt toxins, yet practical field-evolved resistance in H. zea populations and numerous occurrences of unexpected injury occur in Bt crops. In this study, we implemented a network of 73 sentinel sweet corn trials, spanning 16 U.S. states and 4 Canadian provinces, for monitoring changes in H. zea susceptibility to Cry and Vip3A toxins by measuring differences in ear damage and larval infestations between isogenic pairs of non-Bt and Bt hybrids over three years. This approach can monitor susceptibility changes and regional differences in other ear-feeding lepidopteran pests. Temporal changes in the field efficacy of each toxin were evidenced by comparing our current results with earlier published studies, including baseline data for each Bt trait when first commercialized. Changes in amount of ear damage showed significant increases in H. zea resistance to Cry toxins and possibly lower susceptibility to Vip3a. Our findings demonstrate that the sentinel plot approach as an in-field screen can effectively monitor phenotypic resistance and document field-evolved resistance in target pest populations, improving resistance monitoring for Bt crops.
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Affiliation(s)
- G P Dively
- Department of Entomology, University of Maryland, College Park, MD
| | - T P Kuhar
- Department of Entomology, Virginia Tech, Blacksburg, VA
| | - S Taylor
- Department of Entomology, Virginia Tech, Suffolk, VA
| | - H B Doughty
- Virginia Tech ESAREC/Entomology, Painter, VA
| | | | - D Gilrein
- LIHREC, Cornell University, Riverhead, NY
| | - B A Nault
- Department of Entomology, Cornell AgriTech, Geneva, NY
| | | | - J Whalen
- Private IPM Consultant, Millington, MD
| | - D Reisig
- Department of Entomology and Plant Pathology, NC State University, Plymouth, NC
| | | | - S J Fleischer
- Department of Entomology, Penn State University, University Park, PA
| | - David Owens
- University of Delaware Cooperative Extension, Carvel REC, Georgetown, DE
| | - C Welty
- Rothenbuhler Lab, Ohio State University, Columbus, OH
| | - F P F Reay-Jones
- Pee Dee Research and Education Center, Clemson University, Florence, SC
| | - P Porter
- Department of Entomology, Texas A&M University, AgriLife Research and Extension Center, Lubbock, TX
| | - J L Smith
- Field Crop Pest Management, University of Guelph, Ridgetown, Ontario, Canada
| | - J Saguez
- CEROM, 740 Chemin Trudeau, Saint-Mathieu-de-Beloeil, Quebec J3G 0E2, Canada
| | - S Murray
- Perennia Food and Agriculture, Kentville, Nova Scotia, Canada
| | - A Wallingford
- University of New Hampshire Cooperative Extension, Durham, NH
| | - H Byker
- Department of Plant Agriculture, University of Guelph, Winchester, Ontario, Canada
| | - B Jensen
- Department of Entomology, University of Wisconsin, Madison, WI
| | - E Burkness
- Department of Entomology, University of Minnesota, St. Paul, MN
| | - W D Hutchison
- Department of Entomology, University of Minnesota, St. Paul, MN
| | - K A Hamby
- Department of Entomology, University of Maryland, College Park, MD
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